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Yorodumi- PDB-6xcu: NMR structure of Ost4V23D, a critical mutant of Ost4, in DPC micelles -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xcu | ||||||||||||
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Title | NMR structure of Ost4V23D, a critical mutant of Ost4, in DPC micelles | ||||||||||||
Components | Oligosaccharyltransferase | ||||||||||||
Keywords | MEMBRANE PROTEIN / TRANSFERASE | ||||||||||||
Function / homology | Function and homology information oligosaccharyltransferase complex / protein N-linked glycosylation / protein-macromolecule adaptor activity / transferase activity / endoplasmic reticulum membrane / mitochondrion Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | SOLUTION NMR / simulated annealing | ||||||||||||
Authors | Chaudhary, B.P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Glycobiology / Year: 2021 Title: NMR and MD simulations reveal the impact of the V23D mutation on the function of yeast oligosaccharyltransferase subunit Ost4. Authors: Chaudhary, B.P. / Zoetewey, D.L. / McCullagh, M.J. / Mohanty, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xcu.cif.gz | 280.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xcu.ent.gz | 240.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xcu_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 6xcu_full_validation.pdf.gz | 559.2 KB | Display | |
Data in XML | 6xcu_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6xcu_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/6xcu ftp://data.pdbj.org/pub/pdb/validation_reports/xc/6xcu | HTTPS FTP |
-Related structure data
Related structure data | 6xcrC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 5231.000 Da / Num. of mol.: 1 / Mutation: V23D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast) Strain: YJM789 / Gene: OST4, SCY_0690 / Production host: Escherichia coli (E. coli) References: UniProt: A6ZXA2, UniProt: Q99380*PLUS, EC: 2.4.1.119 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 400 uM [U-13C; U-15N] Ost4V23D, 90% H2O/10% D2O Details: 100 mM DPC micelle was added to solubilize the sample Label: 13C, 15N_sample / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 400 uM / Component: Ost4V23D / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Ionic strength: 50 mM / Label: Condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |